Simultaneous profiling of multiple chromatin proteins in the same cells

Gopalan, Sneha; Wang, Yuqing; Harper, Nicholas W.; Garber, Manuel; Fazzio, Thomas G.

doi:10.1101/2021.04.27.441642

Cited by 15 publications

(40 citation statements)

References 43 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Recently, technologies that profile two epigenetic modalities in single cells have been developed 21,22 . These technologies either use proteinA-Tn5 fusion pre-complexed with barcoded oligonucleotides or fusion 21 of Tn5 to HP1a to profile active and repressive chromatin simultaneously 22 . However, these technologies either lack the flexibility to profile various modalities, have lower sensitivity, might present cross-reactivity and/or have not been used to profile complex tissues.…”

Section: Introductionmentioning

confidence: 99%

Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag

Bartošovič

Castelo‐Branco

2022

Preprint

View full text Add to dashboard Cite

Probing epigenomic marks such as histone modifications at a single cell level in thousands of cells has been recently enabled by technologies such as scCUT&Tag. Here we developed a multimodal and optimized iteration of scCUT&Tag called nano-CT (for nano-CUT&Tag) that allows simultaneous probing of three epigenomic modalities at single-cell resolution, using nanobody-Tn5 fusion proteins. nano-CT is compatible with starting materials as low as 25 000 cells and has significantly higher resolution than scCUT&Tag, with a 16-fold increase in the number of fragments per cells. We used nano-CT to simultaneously profile chromatin accessibility, H3K27ac and H3K27me3 in a complex tissue - juvenile mouse brain. The obtained multimodal dataset allowed for discrimination of more cell types/states that scCUT&Tag, and inference of chromatin velocity between ATAC and H3K27ac in the oligodendrocyte (OL) lineage. In addition, we used nano-CT to deconvolute H3K27me3 repressive states and infer two sequential waves of H3K27me3 repression at distinct gene modules during OL lineage progression. Thus, given its high resolution, versatility, and multimodal features, nano-CT allows unique insights in epigenetic landscapes in different biological systems at single cell level.

show abstract

Section: Introductionmentioning

confidence: 99%

Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag

Bartošovič

Castelo‐Branco

2022

Preprint

View full text Add to dashboard Cite

show abstract

“…Recent studies demonstrated the possibility to preload PA-Tn5 with antibodies to target different epigenetic marks simultaneously (Gopalan et al, 2021). We envision that this approach can also be applied to epigenomic MERFISH, making it possible to simultaneous map multiple distinct epigenetic marks in the same cells, for example marking promoter and enhancer activities by measuring H3K4me3 and H3K27ac activities simultaneously to provide a more comprehensive picture of enhancer activity and gene regulation within the cell.…”

Section: Discussionmentioning

confidence: 99%

Spatially resolved epigenomic profiling of single cells in complex tissues

Tian

Ang

Zhuang

2022

Preprint

View full text Add to dashboard Cite

The recent development of spatial omics methods enables single-cell profiling of the transcriptome and the 3D genome organization in a spatially resolved manner. Expanding the repertoire of spatial omics tools, a spatial epigenomics method will accelerate our understanding of the spatial regulation of cell and tissue functions. Here, we report a method for spatially resolved profiling of epigenomes in single cells using in-situ tagmentation and transcription followed by highly multiplexed imaging. We profiled histone modifications marking active promoters and enhancers, H3K4me3 and H3K27ac, and generated high-resolution spatial atlas of hundreds of active promoters and putative enhancers in embryonic and adult mouse brains. Our results further revealed putative promoter-enhancer pairs and enhancer hubs regulating the expression of developmentally important genes. We envision this approach will be generally applicable to spatial profiling of epigenetic modifications and DNA-binding proteins, advancing our understanding of how gene expression is spatiotemporally regulated by the epigenome.

show abstract

“…Reads were mapped to the hg38 genome using bwa-mem2 and fragment files created as described above for the NTT-seq datasets. Code to reproduce this analysis is available on GitHub: https://github.com/timoast/ multi-ct. We ran the CountFragments function in Signac to count the total number of fragments per cell for each multi-CUT&Tag assay, and retained cells with >200 total counts for further analysis, as described in the original publication (Gopalan et al 2021). For mixed-barcode fragments we counted ½ count to the total of each assay matching the pair of Tn5 barcodes.…”

Section: Multi-cutandtag Comparisonmentioning

confidence: 99%

“…2 Extended Data Figure 2. A) Total fragment counts per cell for multiCUT&Tag (Gopalan et al, 2021) and NTT-seq. Fragment counts on y-axis are on a log10 scale.…”

Section: Trajectory Analysismentioning

confidence: 99%

Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolution

Stuart

Hao

Zhang

et al. 2022

Preprint

View full text Add to dashboard Cite

Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility, and other factors. However, most current single-cell-resolution methods are unable to measure more than one aspect of chromatin state in a single experiment, limiting our ability to accurately measure chromatin states. Here, we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), a new assay capable of measuring the genome-wide presence of multiple histone modifications and protein-DNA binding sites at single-cell resolution. NTT-seq utilizes recombinant Tn5 transposase fused to a set of secondary nanobodies (nb). Each nb-Tn5 fusion protein specifically binds to different immunoglobulin-G antibodies, enabling a mixture of primary antibodies binding different epitopes to be used in a single experiment. We apply bulk- and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and in cells of the human immune system, demonstrating the high accuracy and sensitivity of the method. We further extend NTT-seq to enable simultaneous profiling of cell-surface protein expression alongside multimodal chromatin states to study cells of the immune system.

show abstract

Simultaneous profiling of multiple chromatin proteins in the same cells

Cited by 15 publications

References 43 publications

Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag

Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag

Spatially resolved epigenomic profiling of single cells in complex tissues

Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolution

Contact Info

Product

Resources

About